Cellular Systems Dynamics Group PI : Oleg Igoshin

Rice University
Department of Bioengineering - MS142
P.O. Box 1892
Houston, Texas 77251-1892  

Fax:
1(713)3485877

Phone:
1(713)3485502

Links:

- Bioengineering Department
- Rice University
  


(Last modified
December, 2010)

Research Projects

Evolutionary design principles of bacterial stress response

Two-component system architectureWhen exposed to detrimental conditions  such as harsh environment, antibiotics or immune response, bacteria are able to survive by switching their gene expression program to "stress-response" mode. We are interested in understanding overall organization of biochemical networks involved in stress-sensing and responding  in particular model systems as well as formulating general principles of stress-response across bacterial species. Despite conservation of their regulatory core, functional networks responding to stress display variations in their architectures. We want to understand the evolutionary design principles of these networks by in correlating these variations with the different regulatory demands.  In particular, we are interested in the networks characterizing bacterial sigma factors and two-component systems -- two widespread mechanism of master level regulation of bacterial gene expression.  

Bacterial differentiation, bet-hedging and stochastic decision making
Hysteretic switch controls sporulation in B. subtilis

Due to their small size gene expression noise is unavoidable in bacteria. How did they learn to cope with it or use it to their advantages? Using Bacillus subtilis as model system we collaborate with Masaya Fujita(UH)  to study how model bacteria  stochastically decide to undergo sporulation. We are also interested in the ways gene expression noise affects evolution of biochemical network architecture.

Mechanisms and dynamics of genetic regulation in hematopoietic  stem cells

Triad network controlling hematopoetic differentiationAll types of blood cells in our bodies are formed through differentiation of hematopoietic stem cells. Ability of these cells to switch between proliferation and differentiation is determined by the dynamics of their genetic networks. We aim to understand the relationship between feedback architecture of these networks and resulting dynamical properties. We are also interested in general biophysical mechanisms of gene regulation by distant enhancers.

Spatial organization, signaling and motility in bacterial biofilms

Simulations of spiral waves in M. xanthusIn recent years the ubiquity of microbial communities  in nature has become apparent, for instance  most bacteria related to human diseases are associated with biofilms. Myxococcus xanthus is not a pathogen however complex patters formed by these bacteria are often viewed as a model system of multicellular bacterial development. In collaboration with experimental labs of Roy Welch (Syracuse) Larry Shimkets (University of Georgia) and Heidi Kaplan (UTH TMC) we work on using a combination of mathematical modeling and statistical image processing to understand spatial organization and dynamics of the patterns formed by M. xanthus during vegetative and starvation conditions.

Host-pathogen interactions during TB infection

Stress responce netwrok in TBThe bacteria that cause tuberculosis (TB), Mycobacterium tuberculosis, can transition into a dormant state to ward off attacks from antibiotics and the immune system. As a result infection can remain latent for years until the patient is immunocompromised. The mechanisms of switching to and from dormancy require system-level studies of the mutual interaction between host cells and pathogenic bacteria. In collaboration with experimental and clinical microbiologist we aim to uncover the mechanistic basis of the switching.